History on the Biological Nitrogen Fixation Research In
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Azorhizobium Doebereinerae Sp. Nov
ARTICLE IN PRESS Systematic and Applied Microbiology 29 (2006) 197–206 www.elsevier.de/syapm Azorhizobium doebereinerae sp. Nov. Microsymbiont of Sesbania virgata (Caz.) Pers.$ Fa´tima Maria de Souza Moreiraa,Ã, Leonardo Cruzb,Se´rgio Miana de Fariac, Terence Marshd, Esperanza Martı´nez-Romeroe,Fa´bio de Oliveira Pedrosab, Rosa Maria Pitardc, J. Peter W. Youngf aDepto. Cieˆncia do solo, Universidade Federal de Lavras, C.P. 3037 , 37 200–000, Lavras, MG, Brazil bUniversidade Federal do Parana´, C.P. 19046, 81513-990, PR, Brazil cEmbrapa Agrobiologia, antiga estrada Rio, Sa˜o Paulo km 47, 23 851-970, Serope´dica, RJ, Brazil dCenter for Microbial Ecology, Michigan State University, MI 48824, USA eCentro de Investigacio´n sobre Fijacio´n de Nitro´geno, Universidad Nacional Auto´noma de Mexico, Apdo Postal 565-A, Cuernavaca, Mor, Me´xico fDepartment of Biology, University of York, PO Box 373, York YO10 5YW, UK Received 18 August 2005 Abstract Thirty-four rhizobium strains were isolated from root nodules of the fast-growing woody native species Sesbania virgata in different regions of southeast Brazil (Minas Gerais and Rio de Janeiro States). These isolates had cultural characteristics on YMA quite similar to Azorhizobium caulinodans (alkalinization, scant extracellular polysaccharide production, fast or intermediate growth rate). They exhibited a high similarity of phenotypic and genotypic characteristics among themselves and to a lesser extent with A. caulinodans. DNA:DNA hybridization and 16SrRNA sequences support their inclusion in the genus Azorhizobium, but not in the species A. caulinodans. The name A. doebereinerae is proposed, with isolate UFLA1-100 ( ¼ BR5401, ¼ LMG9993 ¼ SEMIA 6401) as the type strain. -
Beijerinckia Derxii Stimulates the Viability of Non-N2-Fixing Bacteria in Nitrogen-Free Media
H.R.Brazilian Barbosa Journal et al. of Microbiology (2000) 31:168-173 ISSN 1517-8382 BEIJERINCKIA DERXII STIMULATES THE VIABILITY OF NON-N2-FIXING BACTERIA IN NITROGEN-FREE MEDIA Heloiza R. Barbosa*; Daniela Strauss Thuler; Márcia Aiko Shirakawa; Natália R. S. Miyasaka Departamento de Microbiologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brasil. Submitted: February 14, 2000; Returned to authors for corrections: May 30, 2000; Approved: August 30, 2000 ABSTRACT The interactions between the nitrogen–fixing microorganism Beijerinckia derxii with two non-diazotrophic bacteria, either Escherichia coli or a facultative sulphur-oxidizing chemolitotroph, were studied in mixed cultures. Direct and indirect contact between B. derxii and E. coli were tested. B. derxii increased CFU numbers and/or maintained the viability of the non-diazotrophic bacteria, but neither growth nor nitrogenase activity of the nitrogen-fixing bacterium were affected by either partner. Key words: Beijerinckia derxii, coculture, viability. INTRODUCTION extent of copper, nickel and ore leaching, indicating that nitrogen fixation can be important in bioextractive metallurgy. Mixed cultures of microorganisms are suitable systems for In this study the N2-fixing microorganism Beijerinckia studying the interactions between organisms and their impact derxii, frequently found in Brazilian acid soils (8) was on the environment and may open up new perspectives that cocultured with two non-N2-fixing bacteria, Escherichia coli could lead to new discoveries. Some mixed cultures containing or a facultative sulphur-oxidizing chemolitotroph, in order to N - fixing bacteria provide conditions more suitable for N 2 2 understand some of the ecological roles of free-living N2-fixing fixation than pure cultures. -
Research Collection
Research Collection Doctoral Thesis Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil Author(s): Ragot, Sabine A. Publication Date: 2016 Permanent Link: https://doi.org/10.3929/ethz-a-010630685 Rights / License: In Copyright - Non-Commercial Use Permitted This page was generated automatically upon download from the ETH Zurich Research Collection. For more information please consult the Terms of use. ETH Library DISS. ETH NO.23284 DEVELOPMENT AND APPLICATION OF MOLECULAR TOOLS TO INVESTIGATE MICROBIAL ALKALINE PHOSPHATASE GENES IN SOIL A thesis submitted to attain the degree of DOCTOR OF SCIENCES of ETH ZURICH (Dr. sc. ETH Zurich) presented by SABINE ANNE RAGOT Master of Science UZH in Biology born on 25.02.1987 citizen of Fribourg, FR accepted on the recommendation of Prof. Dr. Emmanuel Frossard, examiner PD Dr. Else Katrin Bünemann-König, co-examiner Prof. Dr. Michael Kertesz, co-examiner Dr. Claude Plassard, co-examiner 2016 Sabine Anne Ragot: Development and application of molecular tools to investigate microbial alkaline phosphatase genes in soil, c 2016 ⃝ ABSTRACT Phosphatase enzymes play an important role in soil phosphorus cycling by hydrolyzing organic phosphorus to orthophosphate, which can be taken up by plants and microorgan- isms. PhoD and PhoX alkaline phosphatases and AcpA acid phosphatase are produced by microorganisms in response to phosphorus limitation in the environment. In this thesis, the current knowledge of the prevalence of phoD and phoX in the environment and of their taxonomic distribution was assessed, and new molecular tools were developed to target the phoD and phoX alkaline phosphatase genes in soil microorganisms. -
Effectiveness of Biofertilizer Enriched in N by Beijerinckia Indica On
Journal of Soil Science and Plant Nutrition, 2017, 17 (4) 1040-1057 RESEARCH ARTICLE Effectiveness of biofertilizer enriched in N by Beijerinckia indica on sugarcane grown on an Ultisol and the interactive effects between biofertilizer and sugarcane filter cake Fernando Luiz Nunes Oliveira, Wagner Silva Oliveira*, Newton Pereira Stamford, Emmanuella Vila Nova Silva, Carolina Etienne Rosália e Silva Santos and Ana Dolores Santiago Freitas Department of Agronomy, University Federal Rural of Pernambuco, Av. Dom Manoel de Medeiros, s/n°, 52171- 900, Recife, Pernambuco, Brazil. *Corresponding author: [email protected] Abstract To improve yield and nutrient absorption, the addition of fertilizers to provide nutrients in adequate quantities is recommended. An alternative substitution for soluble fertilizer is the use of Acidithiobacillus bacteria to pro- duce rock biofertilizer that is then mixed with organic matter inoculated with diazotrophic bacteria (Beijerinckia indica) for N enrichment. This study evaluates the effectiveness of biofertilizer on nutrient uptake and its inter- action with sugarcane filter cake in field-grown sugarcane on an Ultisol in the Brazilian rainforest region. The experiment used two NPK fertilizer treatments (biofertilizer and soluble fertilizer) applied at three rates (50, 100 and 150% of the recommended rate [RR]) and a control treatment of earthworm compost (20 t ha-1). The fertil- izer treatments were applied with and without filter cake, in four replicates. Total C and N, available P and K, and exchangeable Ca and Mg in plants (upper shoots, leaves and stems) as well as soil samples were analyzed. The biofertilizer showed similar responses as did the soluble fertilizer in nutrient uptake in the different parts of sugarcane and in the soil samples. -
Evolution of Methanotrophy in the Beijerinckiaceae&Mdash
The ISME Journal (2014) 8, 369–382 & 2014 International Society for Microbial Ecology All rights reserved 1751-7362/14 www.nature.com/ismej ORIGINAL ARTICLE The (d)evolution of methanotrophy in the Beijerinckiaceae—a comparative genomics analysis Ivica Tamas1, Angela V Smirnova1, Zhiguo He1,2 and Peter F Dunfield1 1Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada and 2Department of Bioengineering, School of Minerals Processing and Bioengineering, Central South University, Changsha, Hunan, China The alphaproteobacterial family Beijerinckiaceae contains generalists that grow on a wide range of substrates, and specialists that grow only on methane and methanol. We investigated the evolution of this family by comparing the genomes of the generalist organotroph Beijerinckia indica, the facultative methanotroph Methylocella silvestris and the obligate methanotroph Methylocapsa acidiphila. Highly resolved phylogenetic construction based on universally conserved genes demonstrated that the Beijerinckiaceae forms a monophyletic cluster with the Methylocystaceae, the only other family of alphaproteobacterial methanotrophs. Phylogenetic analyses also demonstrated a vertical inheritance pattern of methanotrophy and methylotrophy genes within these families. Conversely, many lateral gene transfer (LGT) events were detected for genes encoding carbohydrate transport and metabolism, energy production and conversion, and transcriptional regulation in the genome of B. indica, suggesting that it has recently acquired these genes. A key difference between the generalist B. indica and its specialist methanotrophic relatives was an abundance of transporter elements, particularly periplasmic-binding proteins and major facilitator transporters. The most parsimonious scenario for the evolution of methanotrophy in the Alphaproteobacteria is that it occurred only once, when a methylotroph acquired methane monooxygenases (MMOs) via LGT. -
Unesco – Eolss Sample Chapters
BIOTECHNOLOGY – Vol VIII - Essentials of Nitrogen Fixation Biotechnology - James H. P. Kahindi, Nancy K. Karanja ESSENTIALS OF NITROGEN FIXATION BIOTECHNOLOGY James H. P. Kahindi United States International University, Nairobi, KENYA Nancy K. Karanja Nairobi Microbiological Resources Centre, University of Nairobi, KENYA Keywords: Rhizobium, Bradyrhizobium, Sinorhizobium, Azorhizobium, Legumes, Nitrogen Fixation Contents 1. Introduction 2. Crop Requirements for Nitrogen 3. Potential for Biological Nitrogen Fixation [BNF] Systems 4. Diversity of Rhizobia 4.l. Factors Influencing Biological Nitrogen Fixation [BNF] 5. The Biochemistry of Biological Nitrogen Fixation: The Nitrogenase System 5.1. The Molybdenum Nitrogenase System 5.1.1. The Iron Protein (Fe protein) 5.1.2. The MoFe Protein 5.2. The Vanadium Nitrogenase 5.3. Nitrogenase-3 6. The Genetics of Nitrogen Fixation 6.1. The Mo-nitrogenase Structural Genes (nif H,D,K) 6.2. Genes for nitrogenase-2 (vnf H,D,G,K,vnfA,vnfE,N,X) 6.3. Regulation of Nif Gene Expression 7. The Potential for Biological Nitrogen Fixation with Non-legumes 7.1. Frankia 7.2. Associative Nitrogen Fixation 8. Application of Biological Nitrogen Fixation Technology 8.1. Experiences of the Biological Nitrogen Fixation -MIRCENs 8.2 Priorities for Action Glossary UNESCO – EOLSS Bibliography Biographical Sketches Summary SAMPLE CHAPTERS Nitrogen constitutes 78% of the Earth’s atmosphere, yet it is frequently the limiting nutrient to agricultural productivity. This necessitates the addition of nitrogen to the soil either through industrial nitrogen fertilizers, which is accomplished at a substantial energy cost, or by transformation of atmospheric nitrogen into forms which plants can take up for protein synthesis. This latter form is known as biological nitrogen fixation and is accomplished by free-living and symbiotic microorganisms endowed with the enzyme nitrogenase. -
Supplement of Biogeosciences, 13, 175–190, 2016 Doi:10.5194/Bg-13-175-2016-Supplement © Author(S) 2016
Supplement of Biogeosciences, 13, 175–190, 2016 http://www.biogeosciences.net/13/175/2016/ doi:10.5194/bg-13-175-2016-supplement © Author(s) 2016. CC Attribution 3.0 License. Supplement of Co-occurrence patterns in aquatic bacterial communities across changing permafrost landscapes J. Comte et al. Correspondence to: J. Comte ([email protected]) The copyright of individual parts of the supplement might differ from the CC-BY 3.0 licence. Supplementary information Figures Figure S1: UPGMA clustering based on unweighted UniFrac distances among bacterial community samples. Color refers to valley identity with SAS: brown, KWK: purple, BGR: green, NAS: orange, RBL: blue. The complete names of the valleys are given in the main text. Figure S2: Rank abundance curve of the bacterial communities originating from the 5 different valleys. Color refers to valley identity with SAS: brown, KWK: purple, BGR: green, NAS: orange, RBL: blue. The complete names of the valleys are given in the text. Figure S3: Taxonomic uniqueness as determined by the local contribution to β -diversity (LCBD) among the different sampled valleys. The solid black horizontal and vertical lines represent the mean and standard deviation respectively. Figure S4: Heatmap representation of habitat preference of the 2166 bacterial OTUs detected in the dataset. Habitat preference was determined by point biserial correlation. Figure S5: Association networks between co-occurring bacterial OTUs and with the abiotic and biotic local conditions based on maximum interaction coefficient (MIC). Significant associations (MIC> 0.44, Pfdr<0.03) are presented. The color of the edges refers to the strengths of the relationship between two nodes and is proportional to MIC values with black lines corresponding to strong links). -
Bacterial Soil Rejuvenation, a Process to Initiate Viridescence, Restoration and Repair of Natural Resources Damaged by Mining That Impact Butte Area One
Bacterial Soil Rejuvenation, A Process to Initiate Viridescence, Restoration and Repair of Natural Resources Damaged by Mining that Impact Butte Area One A Proposal to the Montana BNRC/NRDP November 15, 2016 Dr. Grant G. Mitman Research Professor Montana Tech of The University of Montana 1300 West Park Street, Butte MT 59701 [email protected] 406-496-4617, 406-490-3177 (cell) http://bacmap.wishartlab.com/system/images/681/medium/Beijerinckia_indica.jpg?1319706411 https://microbewiki.kenyon.edu/images/thumb/9/9f/Slime.jpg/200px-Slime.jpg https://www.planetnatural.com/product/azos-nitrogen-fixing- microbes/ "Here is the means to end the great extinction spasm. The next century will, I believe, be the era of restoration in ecology."- E.O. Wilson VIRIDESCENCE - Stock World http://www.ofoto-gallery.com/packs.php?in=9&id=1376&lang=en Restoration and Repair of Natural Resources Damaged by Mining that Impact Butte Area One A. Contact Information Dr. Grant G. Mitman Research Professor Montana Tech of The University of Montana 1300 West Park Street, Butte MT 59701 [email protected] 406-496-4617, 406-490-3177 (cell) B.1. Project Summary and Map Microbial Biorestoration is the practice of renewing and restoring degraded, damaged, or destroyed soil ecosystems by active human intervention. In the case of Butte, Montana that soil ecosystem was destroyed by mining activities and/or the subsequent deposition of tailings which stripped the soil of organic carbon and indigenous bacteria. As a result, the soil ecosystem died; it has lost its ability to recycle essential nutrients through normal biogeochemical processes, thus preventing most plant life and other organisms from growing. -
Beijerinckia Derxii Releases Plant Growth Regulators and Amino Acids in Synthetic Media Independent of Nitrogenase Activity
Journal of Applied Microbiology 2003, 95, 799–806 doi:10.1046/j.1365-2672.2003.02047.x Beijerinckia derxii releases plant growth regulators and amino acids in synthetic media independent of nitrogenase activity D.S. Thuler1, E.I.S. Floh2, W. Handro2 and H.R. Barbosa1 1Department of Microbiology, Institute of Biomedical Sciences, University of Saao~ Paulo, Saao~ Paulo, Brasil, and 2Department of Botany, Institute of Biosciences, University of Saao~ Paulo, Saao~ Paulo, Brasil 2002/339: received 3 September 2002, revised 2 May 2003 and accepted 23 May 2003 ABSTRACT D. S. TH UL ER , E . I. S . FL OH , W . H AN DR O A ND H . R. B AR BOS A. 2003. Aims: This study aims at evaluating the ability of Beijerinckia derxii, a free-living nitrogen (N)-fixing bacterium frequently isolated from tropical soils, to release certain plant growth regulators [indoleacetic acid (IAA), ethylene, polyamines] and amino acids into the growth medium. Methods and Results: The production of those substances was compared using both cultures in which nitrogenase was active (N-free medium) and cultures in which nitrogenase was repressed (combined-N cultures). Those cultures were grown under agitation and in absence of agitation. Total IAA production was higher in agitated, N-free cultures but specific production was greater in combined-N cultures under agitation. Putrescine and spermidine were detected under all conditions tested. Ethylene was produced in both N-free and combined-N cultures. A greatest diversity of amino acids was released in N-free cultures. Conclusions: There was no inhibition of the production of the analysed substances under conditions where nitrogenase was inactive. -
High Throughput Sequencing to Detect Differences In
Microorganisms 2015, 3, 113-136; doi:10.3390/microorganisms3020113 OPEN ACCESS microorganisms ISSN 2076-2607 www.mdpi.com/journal/microorganisms Article High Throughput Sequencing to Detect Differences in Methanotrophic Methylococcaceae and Methylocystaceae in Surface Peat, Forest Soil, and Sphagnum Moss in Cranesville Swamp Preserve, West Virginia, USA Evan Lau *, Edward J. Nolan IV, Zachary W. Dillard, Ryan D. Dague, Amanda L. Semple and Wendi L. Wentzell Department of Natural Sciences and Mathematics, West Liberty University, 208 University Drive, CUB#139, West Liberty, WV 26074, USA; E-Mails: [email protected] (E.J.N.); [email protected] (Z.W.D.); [email protected] (R.D.D.); [email protected] (A.L.S.); [email protected] (W.L.W.) * Author to whom correspondence should be addressed; E-Mail: [email protected] or [email protected]; Tel.: +1-304-336-8529. Academic Editors: Marina G. Kalyuzhnaya and Ludmila Chistoserdova Received: 25 January 2015/ Accepted: 26 March 2015 / Published: 2 April 2015 Abstract: Northern temperate forest soils and Sphagnum-dominated peatlands are a major source and sink of methane. In these ecosystems, methane is mainly oxidized by aerobic methanotrophic bacteria, which are typically found in aerated forest soils, surface peat, and Sphagnum moss. We contrasted methanotrophic bacterial diversity and abundances from the (i) organic horizon of forest soil; (ii) surface peat; and (iii) submerged Sphagnum moss from Cranesville Swamp Preserve, West Virginia, using multiplex sequencing of bacterial 16S rRNA (V3 region) gene amplicons. From ~1 million reads, >50,000 unique OTUs (Operational Taxonomic Units), 29 and 34 unique sequences were detected in the Methylococcaceae and Methylocystaceae, respectively, and 24 potential methanotrophs in the Beijerinckiaceae were also identified. -
Reclassification of Beijerinckia Fluminensis CIP 106281T and Beijerinckia
1 Reclassification of Beijerinckia fluminensis CIP 106281T and Beijerinckia 2 fluminensis UQM 1685T as Rhizobium radiobacter strains, and proposal of 3 Beijerinckia fluminensis LMG 2819 as Beijerinckia doebereinerae sp. nov. 4 5 Monike Oggerin1, David R. Arahal2, Víctor Rubio3, Irma Marín1* 6 7 1Centro de Biología Molecular Severo Ochoa, Universidad Autónoma de Madrid, Cantoblanco, 8 28049 Madrid, Spain 9 2Spanish Type Culture Collection (CECT) and Department of Microbiology and Ecology, 10 University of Valencia, Campus de Burjassot, 46100 Valencia, Spain 11 3Instituto de Ciencias Agrarias, Centro de Ciencias Medio Ambientales, CSIC, 28006 Madrid, 12 Spain 13 14 15 Running title: Beijerinckia doebereinerae sp. nov. 16 17 Correspondence: Irma Marín 18 e-mail: [email protected]. Phone: +34 914978078. Fax: +34 914978300 19 20 ……………………………………………………………………………………………………… 21 Footnote: The GenBank/EMBL/DDBJ accession number for the 16S rRNA gene sequence of 22 strain LMG 2819T, UQM 1685 and CIP 106281 are EU401905, EU401907 and EU401908 23 respectively. 24 Transmission electron micrographs of strains LMG 2819T and UQM 1685 are available as a 25 supplementary figure in IJSEM Online. 26 26 During the course of a research project with free-living nitrogen fixing bacteria we 27 determined the 16S rRNA gene sequence of strains Beijerinckia fluminensis UQM 1685T 28 and B. fluminensis CIP 106281T and discovered that they were only 90.6-91.2 % similar to 29 the sequences of other Beijerinckia species and subspecies. Moreover, the highest 30 similarity to these sequences (99.7 %) corresponded to Rhizobium radiobacter (including 31 Agrobacterium tumefaciens). Other diagnostic features confirmed that both strains have 32 the same origin but do not descend from the nomenclatural type. -
1 Alphaproteobacteria Fix Nitrogen in a Sphagnum-Dominated Peat Bog Using Molybdenum
bioRxiv preprint doi: https://doi.org/10.1101/114918; this version posted March 7, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Alphaproteobacteria fix nitrogen in a Sphagnum-dominated peat bog using molybdenum- 2 dependent nitrogenase 3 Melissa J. Warren1*, Xueju Lin2**, John C. Gaby2***, Cecilia B. Kretz1****, Peter L. Morton3, 4 Jennifer Pett-Ridge4, David J. Weston5, Christopher W. Schadt5, Joel E. Kostka1,2, Jennifer B. 5 Glass1,2# 6 7 1School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA 8 2School of Biology, Georgia Institute of Technology, Atlanta, GA, USA 9 3Department of Earth, Ocean and Atmospheric Science, Florida State University, Tallahassee, 10 Florida, USA 11 4Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, Livermore, 12 CA, USA 13 5Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA 14 15 Now at: *CH2M, Atlanta, GA, USA; **InstantLabs, Baltimore, MD, USA; ***Faculty of 16 Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Oslo, 17 Norway; ****Division of Bacterial Diseases, National Center for Immunization and Respiratory 18 Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA 19 #Corresponding author: Jennifer B. Glass, 404-894-3942; [email protected] 20 21 Running Title: Molybdenum-based nitrogen fixation in a Sphagnum peat bog 1 bioRxiv preprint doi: https://doi.org/10.1101/114918; this version posted March 7, 2017.